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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ), 'gf_id' => 'HOM05D001132', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001132' ), 'data_identifier' => 'HOM05D001132', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001132', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p29930' => 'bna', 'A03p05240' => 'bna', 'A06p45950' => 'bna', 'A06p46440' => 'bna', 'A07p10230' => 'bna', 'A07p10240' => 'bna', 'A08p24850' => 'bna', 'A08p24860' => 'bna', 'A09p36680' => 'bna', 'A10p25920' => 'bna', 'Aa31LG3G15340' => 'aar', 'Aa31LG6G5850' => 'aar', 'Aa31LG6G840' => 'aar', 'Aa31LG9G6440' => 'aar', 'Aa31LG9G7360' => 'aar', 'Actinidia07670' => 'ach', 'Actinidia08074' => 'ach', 'Actinidia16743' => 'ach', 'Actinidia19492' => 'ach', 'Actinidia30651' => 'ach', 'Actinidia35610' => 'ach', 'Actinidia39547' => 'ach', 'Ah.03g136170' => 'amhyb', 'Ah.09g232930' => 'amhyb', 'Ah.14g084300' => 'amhyb', 'AL1G43600' => 'aly', 'AL1G43610' => 'aly', 'AL6G22620' => 'aly', 'AL7G36290' => 'aly', 'AL8G12000' => 'aly', 'AL8G12950' => 'aly', 'Aqoxy1G01845' => 'aox', 'Aqoxy1G01935' => 'aox', 'Aqoxy5G03382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.37RBIB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.40WTVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MM49L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C64WWP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8KF1C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EH7R8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WV8VEA' => 'arhy', 'AT1G29770' => 'ath', 'AT1G29780' => 'ath', 'AT4G18140' => 'ath', 'AT5G11860' => 'ath', 'AT5G45700' => 'ath', 'AT5G46410' => 'ath', 'ATR0213G032' => 'atr', 'ATR0561G277' => 'atr', 'ATR0582G163' => 'atr', 'ATR0693G227' => 'atr', 'Atru.chr10.1390' => 'acertr', 'Atru.chr10.1524' => 'acertr', 'Atru.chr11.2318' => 'acertr', 'Atru.chr12.1117' => 'acertr', 'Atru.chr4.3038' => 'acertr', 'AUR62005618' => 'cqu', 'AUR62024112' => 'cqu', 'AUR62027556' => 'cqu', 'AUR62035800' => 'cqu', 'AUR62039496' => 'cqu', 'AUR62041803' => 'cqu', 'BcaB01g05449' => 'bca', 'BcaB03g12177' => 'bca', 'BcaB03g12178' => 'bca', 'BcaB03g13859' => 'bca', 'BcaB07g32564' => 'bca', 'BcaC01g00136' => 'bca', 'BcaC01g00137' => 'bca', 'BcaC04g19191' => 'bca', 'BcaC05g26992' => 'bca', 'BcaC06g31526' => 'bca', 'BcaC06g34410' => 'bca', 'BcaC06g35463' => 'bca', 'BcaC06g35464' => 'bca', 'BolC3t19873H' => 'bol', 'BolC3t19874H' => 'bol', 'BolC5t31576H' => 'bol', 'BolC7t42067H' => 'bol', 'BolC7t42068H' => 'bol', 'BolC7t43417H' => 'bol', 'BolC7t43516H' => 'bol', 'BolC9t59328H' => 'bol', 'BraA02t08015Z' => 'bra', 'BraA03t09863Z' => 'bra', 'BraA06t27459Z' => 'bra', 'BraA06t27517Z' => 'bra', 'BraA07t28819Z' => 'bra', 'BraA07t28820Z' => 'bra', 'BraA08t34440Z' => 'bra', 'BraA08t34441Z' => 'bra', 'BraA09t39187Z' => 'bra', 'BraA10t44654Z' => 'bra', 'C03p06030' => 'bna', 'C03p76170' => 'bna', 'C03p76180' => 'bna', 'C05p28520' => 'bna', 'C07p15750' => 'bna', 'C07p15760' => 'bna', 'C07p28810' => 'bna', 'C07p29640' => 'bna', 'C09p65000' => 'bna', 'CAN.G257.47' => 'can', 'CAN.G333.11' => 'can', 'CAN.G37.5' => 'can', 'CAN.G411.31' => 'can', 'CAN.G502.20' => 'can', 'CANSAT01G0010' => 'cansat', 'CANSAT35G1123' => 'cansat', 'CANSAT35G1824' => 'cansat', 'CARHR029140' => 'chi', 'CARHR029150' => 'chi', 'CARHR175350' => 'chi', 'CARHR175360' => 'chi', 'CARHR176270' => 'chi', 'CARHR201300' => 'chi', 'CARHR224880' => 'chi', 'Carub.0001s2801' => 'cru', 'Carub.0001s2802' => 'cru', 'Carub.0006s1039' => 'cru', 'Carub.0008s0148' => 'cru', 'Carub.0008s0231' => 'cru', 'Ca_00481_v3' => 'car', 'Ca_02506_v3' => 'car', 'Ca_14015_v3' => 'car', 'Ca_16462_v3' => 'car', 'CBR_g24286' => 'cbr', 'CBR_g28529' => 'cbr', 'CBR_g46276' => 'cbr', 'Cc00_g03260' => 'ccan', 'Cc02_g15810' => 'ccan', 'Cc11_g16870' => 'ccan', 'CDE03G0090' => 'cde', 'CDE03G0385' => 'cde', 'CDE04G1969' => 'cde', 'CDE04G2396' => 'cde', 'CDE05G1086' => 'cde', 'CDE07G1347' => 'cde', 'Cfa001014' => 'cfa', 'Cfa001017' => 'cfa', 'Cfa021996' => 'cfa', 'Ciclev10001022m.g' => 'ccl', 'Ciclev10005213m.g' => 'ccl', 'Ciclev10016072m.g' => 'ccl', 'Ciclev10016126m.g' => 'ccl', 'Ciclev10018393m.g' => 'ccl', 'Ciclev10031713m.g' => 'ccl', 'CiPaw.05G110200' => 'cil', 'CiPaw.06G102400' => 'cil', 'CiPaw.09G129100' => 'cil', 'CiPaw.09G136300' => 'cil', 'CiPaw.10G095900' => 'cil', 'CiPaw.10G102800' => 'cil', 'ClCG01G023990' => 'cla', 'ClCG01G024260' => 'cla', 'ClCG08G017120' => 'cla', 'COL.COLO4_20396' => 'col', 'COL.COLO4_22795' => 'col', 'COL.COLO4_22853' => 'col', 'COL.COLO4_31210' => 'col', 'Cpa.g.sc124.11' => 'cpa', 'Cpa.g.sc17.121' => 'cpa', 'Cpa.g.sc43.52' => 'cpa', 'Cpa.g.sc43.53' => 'cpa', 'Cre06.g284450' => 'cre', 'Cre07.g323850' => 'cre', 'Cre07.g323900' => 'cre', 'Cre09.g391541' => 'cre', 'CsaV3_6G051130' => 'csa', 'CsaV3_6G051420' => 'csa', 'CSS0006026' => 'camsi', 'CSS0012126' => 'camsi', 'CSS0012982' => 'camsi', 'CSS0024826' => 'camsi', 'CSS0026166' => 'camsi', 'CSS0029043' => 'camsi', 'CSS0030919' => 'camsi', 'DCAR_007910' => 'dca', 'DCAR_027968' => 'dca', 'Dinv12734' => 'din', 'Dinv14838' => 'din', 'Dinv17560' => 'din', 'Dinv30679' => 'din', 'Dinv32296' => 'din', 'Duzib160G0018' => 'dzi', 'Duzib160G0372' => 'dzi', 'Duzib160G0763' => 'dzi', 'Duzib192G0319' => 'dzi', 'Duzib235G0153' => 'dzi', 'Duzib235G0339' => 'dzi', 'Duzib235G1105' => 'dzi', 'Duzib235G1510' => 'dzi', 'Duzib251G0943' => 'dzi', 'Duzib268G1627' => 'dzi', 'ECA232G3386' => 'eca', 'ECA233G4869' => 'eca', 'ECA234G2476' => 'eca', 'ECA234G4105' => 'eca', 'ECA236G1960' => 'eca', 'ECA238G3282' => 'eca', 'EL10Ac5g12110' => 'bvu', 'EL10Ac6g13500' => 'bvu', 'EL10Ac8g19791' => 'bvu', 'EL10Ac8g19875' => 'bvu', 'Eucgr.D00426' => 'egr', 'Eucgr.E02354' => 'egr', 'Eucgr.H04641' => 'egr', 'Eucgr.J00321' => 'egr', 'FAN07G2966' => 'fan', 'FAN11G0010' => 'fan', 'FAN11G1984' => 'fan', 'FAN12G4028' => 'fan', 'FAN16G0558' => 'fan', 'FAN16G2409' => 'fan', 'FAN17G0440' => 'fan', 'FAN21G2263' => 'fan', 'FAN21G3968' => 'fan', 'FAN21G4032' => 'fan', 'FAN25G2714' => 'fan', 'FAN25G3231' => 'fan', 'FvH4_3g06370' => 'fve', 'FvH4_3g07100' => 'fve', 'FvH4_3g07110' => 'fve', 'FvH4_3g36710' => 'fve', 'FvH4_4g23810' => 'fve', 'Glyma.04G128700' => 'gma', 'Glyma.06G314700' => 'gma', 'Glyma.09G088300' => 'gma', 'Glyma.11G250300' => 'gma', 'Glyma.13G225100' => 'gma', 'Glyma.15G087100' => 'gma', 'Glyma.15G196400' => 'gma', 'Glyma.18G006900' => 'gma', 'Gohir.A01G162800' => 'ghi', 'Gohir.A06G128002' => 'ghi', 'Gohir.A06G135600' => 'ghi', 'Gohir.A10G033500' => 'ghi', 'Gohir.A10G033550' => 'ghi', 'Gohir.A10G033600' => 'ghi', 'Gohir.A10G037900' => 'ghi', 'Gohir.D01G147800' => 'ghi', 'Gohir.D06G139100' => 'ghi', 'Gohir.D06G139150' => 'ghi', 'Gohir.D06G139200' => 'ghi', 'Gohir.D06G139250' => 'ghi', 'Gohir.D06G140800' => 'ghi', 'Gohir.D10G034200' => 'ghi', 'Gohir.D10G034250' => 'ghi', 'Gohir.D10G034300' => 'ghi', 'Gohir.D10G038900' => 'ghi', 'Gorai.002G183900' => 'gra', 'Gorai.010G161800' => 'gra', 'Gorai.010G161900' => 'gra', 'Gorai.010G162000' => 'gra', 'Gorai.010G162100' => 'gra', 'Gorai.010G162300' => 'gra', 'Gorai.010G164300' => 'gra', 'Gorai.011G035900' => 'gra', 'Gorai.011G036000' => 'gra', 'Gorai.011G036100' => 'gra', 'Gorai.011G041000' => 'gra', 'GSVIVG01001951001' => 'vvi', 'GSVIVG01010477001' => 'vvi', 'GSVIVG01021382001' => 'vvi', 'HanXRQChr04g0118421' => 'han', 'HanXRQChr08g0207771' => 'han', 'HanXRQChr12g0372211' => 'han', 'HanXRQChr15g0480011' => 'han', 'HanXRQChr16g0520581' => 'han', 'HanXRQChr16g0520591' => 'han', 'HanXRQChr16g0520601' => 'han', 'HanXRQChr17g0564941' => 'han', 'Haze_05365' => 'cav', 'Haze_05491' => 'cav', 'Haze_12415' => 'cav', 'Hma1.2p1_0015F.1_g010370' => 'hma', 'HPP92_001996' => 'vpl', 'HPP92_003564' => 'vpl', 'HPP92_010047' => 'vpl', 'HPP92_020062' => 'vpl', 'Hund21478' => 'sun', 'Hund25463' => 'sun', 'Lalb_Chr07g0186071' => 'lal', 'Lalb_Chr08g0233311' => 'lal', 'Lalb_Chr11g0075751' => 'lal', 'Lalb_Chr12g0204741' => 'lal', 'Lalb_Chr18g0054911' => 'lal', 'Lj1A1182G77' => 'lonja', 'Lj1P1177T78' => 'lonja', 'Lj2A311T61' => 'lonja', 'Lj2P316T22' => 'lonja', 'Lj3A1068T39' => 'lonja', 'Lj3g0002916' => 'lja', 'Lj6g0007387' => 'lja', 'Lj6g0008847' => 'lja', 'Lj6g0027192' => 'lja', 'Lsat_1_v5_gn_4_28020' => 'lsa', 'Lsat_1_v5_gn_7_30960' => 'lsa', 'Lsat_1_v5_gn_8_135541' => 'lsa', 'Lsat_1_v5_gn_8_135561' => 'lsa', 'Lsat_1_v5_gn_8_147640' => 'lsa', 'Manes.12G011700' => 'mes', 'Manes.15G117300' => 'mes', 'Manes.16G043800' => 'mes', 'Manes.17G061000' => 'mes', 'Manes.17G065100' => 'mes', 'Mapoly0008s0118' => 'mpo', 'Mapoly0046s0042' => 'mpo', 'Mapoly0046s0100' => 'mpo', 'Mapoly0224s0008' => 'mpo', 'MBI06_g16568_MAGBIO' => 'mbi', 'MBI07_g31016_MAGBIO' => 'mbi', 'MBI10_g02379_MAGBIO' => 'mbi', 'MBI19_g03255_MAGBIO' => 'mbi', 'MCO11G874' => 'mco', 'MCO12G163' => 'mco', 'MD00G1007300' => 'mdo', 'MD00G1007500' => 'mdo', 'MD05G1291500' => 'mdo', 'MD10G1267500' => 'mdo', 'MD10G1273900' => 'mdo', 'MD10G1274000' => 'mdo', 'MD13G1118600' => 'mdo', 'MD16G1118800' => 'mdo', 'Medtr2g017810' => 'mtr', 'Medtr2g049420' => 'mtr', 'Medtr3g006690' => 'mtr', 'Medtr3g085395' => 'mtr', 'Medtr3g085400' => 'mtr', 'Medtr5g045920' => 'mtr', 'Medtr8g041980' => 'mtr', 'MELO3C007164.2' => 'cme', 'MELO3C007191.2' => 'cme', 'MELO3C010744.2' => 'cme', 'Migut.H01403' => 'egut', 'Migut.K00731' => 'egut', 'Migut.M00957' => 'egut', 'MSTRG.13238' => 'ama', 'MSTRG.14757' => 'ama', 'MSTRG.16202' => 'ama', 'MSTRG.7456' => 'ama', 'MSTRG.8001' => 'ama', 'Nitab4.5_0001394g0020' => 'nta', 'Nitab4.5_0001778g0140' => 'nta', 'Nitab4.5_0007306g0020' => 'nta', 'Nitab4.5_0008001g0020' => 'nta', 'Nitab4.5_0008572g0010' => 'nta', 'Nn3g16466' => 'nnu', 'Nn3g20897' => 'nnu', 'Nn4g22330' => 'nnu', 'Nn6g34452' => 'nnu', 'Oeu040947.3' => 'oeu', 'Oeu041665.1' => 'oeu', 'Oeu042432.1' => 'oeu', 'Oeu058921.1' => 'oeu', 'Os01g0629400' => 'osa', 'Os01g0665300' => 'osa', 'Os03g0850100' => 'osa', 'Os05g0205100' => 'osa', 'Os05g0566200' => 'osa', 'Os07g0207700' => 'osa', 'Peaxi162Scf00076g00111' => 'pax', 'Peaxi162Scf00112g00133' => 'pax', 'Peaxi162Scf00145g02011' => 'pax', 'Peaxi162Scf00242g00225' => 'pax', 'Peaxi162Scf00570g00214' => 'pax', 'PGR031G1412' => 'pgr', 'PGR044G0895' => 'pgr', 'PGSC0003DMG400003085' => 'stu', 'PGSC0003DMG400017678' => 'stu', 'PGSC0003DMG400028411' => 'stu', 'Phvul.001G261600' => 'pvu', 'Phvul.004G152900' => 'pvu', 'Phvul.006G171200' => 'pvu', 'Phvul.008G162100' => 'pvu', 'Phvul.009G213700' => 'pvu', 'Potri.001G054700' => 'ptr', 'Potri.001G353700' => 'ptr', 'Potri.003G173700' => 'ptr', 'Potri.004G062900' => 'ptr', 'Potri.011G072000' => 'ptr', 'Potri.011G078300' => 'ptr', 'Pp3c8_21120' => 'ppa', 'PRCOL_00000302' => 'pco', 'PRCOL_00003623' => 'pco', 'Prupe.1G226400' => 'ppe', 'Prupe.4G068500' => 'ppe', 'Prupe.4G068600' => 'ppe', 'Prupe.4G074000' => 'ppe', 'Psat1g020160' => 'psa', 'Psat1g196760' => 'psa', 'Psat5g096320' => 'psa', 'Psat5g230440' => 'psa', 'PSO017G0354' => 'pso', 'PSO017G3080' => 'pso', 'PSO421G0042' => 'pso', 'PSO478G2499' => 'pso', 'PSO478G4666' => 'pso', 'PSO541G6103' => 'pso', 'PSO675G6501' => 'pso', 'PSO675G8060' => 'pso', 'PSO724G0244' => 'pso', 'PSO782G2624' => 'pso', 'QL03p052811' => 'qlo', 'QL05p050221' => 'qlo', 'QL05p060405' => 'qlo', 'QL93p1081_0004' => 'qlo', 'RcHm_v2.0_Chr4g0430361' => 'rch', 'RcHm_v2.0_Chr5g0012001' => 'rch', 'RcHm_v2.0_Chr5g0012011' => 'rch', 'RcHm_v2.0_Chr5g0012931' => 'rch', 'Rhsim02G0152500' => 'rsi', 'Rhsim12G0026100' => 'rsi', 'Rhsim13G0033200' => 'rsi', 'Rhsim13G0187000' => 'rsi', 'Sabra01G0039200' => 'sbr', 'Sabra01G0164200' => 'sbr', 'Sabra03G0127200' => 'sbr', 'Sabra04G0041700' => 'sbr', 'Sabra11G0056400' => 'sbr', 'Sabra11G0059700' => 'sbr', 'Sabra16G0232600' => 'sbr', 'SalBow2G2467' => 'sbo', 'SalBow5G1191' => 'sbo', 'SalBow5G4338' => 'sbo', 'SalBow7G2368' => 'sbo', 'SalBow7G3587' => 'sbo', 'SalBow8G0577' => 'sbo', 'SalBow8G3036' => 'sbo', 'Sc04g0010110' => 'sci', 'Sc17g0005220' => 'sci', 'Sc17g0005570' => 'sci', 'Sed0015151' => 'sed', 'Sed0015299' => 'sed', 'Sed0015837' => 'sed', 'Sed0019545' => 'sed', 'SEGI_01844' => 'sgi', 'SEGI_09746' => 'sgi', 'SEGI_15066' => 'sgi', 'SEGI_26505' => 'sgi', 'SEGI_35065' => 'sgi', 'SEGI_37355' => 'sgi', 'SGA_v2.0_scaffold106G30608' => 'sas', 'SGA_v2.0_scaffold1G00136' => 'sas', 'SGA_v2.0_scaffold333G49021' => 'sas', 'SGA_v2.0_scaffold9G04689' => 'sas', 'SHI17961' => 'shi', 'SMO087G0001' => 'smo', 'SMO087G0002' => 'smo', 'SMO114G0044' => 'smo', 'SMO116G0187' => 'smo', 'SMO116G0424' => 'smo', 'SMO139G0107' => 'smo', 'SMO141G0041' => 'smo', 'SMO141G0226' => 'smo', 'SMO144G0022' => 'smo', 'SMO164G0081' => 'smo', 'SMO201G0017' => 'smo', 'SMO201G0182' => 'smo', 'SMO201G0197' => 'smo', 'SMO239G0159' => 'smo', 'SMO266G0030' => 'smo', 'SMO270G0112' => 'smo', 'SMO271G0009' => 'smo', 'SMO271G0032' => 'smo', 'SMO271G0034' => 'smo', 'SMO271G0081' => 'smo', 'SMO271G0083' => 'smo', 'SMO271G0087' => 'smo', 'SMO271G0110' => 'smo', 'SMO271G0122' => 'smo', 'SMO271G0156' => 'smo', 'SMO271G0161' => 'smo', 'SMO271G0188' => 'smo', 'SMO292G0004' => 'smo', 'SMO308G0032' => 'smo', 'SMO308G0060' => 'smo', 'SMO334G0135' => 'smo', 'SMO335G0002' => 'smo', 'SMO335G0018' => 'smo', 'SMO337G0075' => 'smo', 'SMO339G0009' => 'smo', 'SMO347G0101' => 'smo', 'SMO364G0774' => 'smo', 'SMO367G0118' => 'smo', 'SMO367G1061' => 'smo', 'Solyc02g071250.3' => 'sly', 'Solyc02g071930.2' => 'sly', 'Solyc04g045630.3' => 'sly', 'Sopen02g020310' => 'spe', 'Sopen02g020920' => 'spe', 'Sopen04g017590' => 'spe', 'Sp1g25660' => 'spa', 'Sp1g25670' => 'spa', 'Sp2g10590' => 'spa', 'Sp2g11260' => 'spa', 'Sp6g31740' => 'spa', 'TAR624G1169' => 'tar', 'TAR626G0215' => 'tar', 'TAR627G0181' => 'tar', 'TAR629G0892' => 'tar', 'TAR633G0761' => 'tar', 'THA.LOC104798443' => 'tha', 'THA.LOC104806114' => 'tha', 'THA.LOC104812659' => 'tha', 'THA.LOC104812883' => 'tha', 'THA.LOC104820702' => 'tha', 'THA.LOC104820703' => 'tha', 'THA.LOC104824644' => 'tha', 'Thecc.02G209300' => 'tca', 'Thecc.06G157400' => 'tca', 'Thecc.06G163400' => 'tca', 'Thecc.06G163500' => 'tca', 'Thecc.06G163600' => 'tca', 'Thhalv10000883m.g' => 'esa', 'Thhalv10000984m.g' => 'esa', 'Thhalv10009586m.g' => 'esa', 'Thhalv10009741m.g' => 'esa', 'Thhalv10014204m.g' => 'esa', 'Thhalv10019804m.g' => 'esa', 'TPR.G17997' => 'tpr', 'TPR.G25528' => 'tpr', 'TPR.G28284' => 'tpr', 'TPR.G4569' => 'tpr', 'TWI09G1026' => 'twi', 'TWI09G1552' => 'twi', 'TWI18G0246' => 'twi', 'TWI53G0651' => 'twi', 'TWI53G2106' => 'twi', 'TWI75G1530' => 'twi', 'unitig_22.g6406' => 'ugi', 'unitig_26.g10091' => 'ugi', 'unitig_749.g13670' => 'ugi', 'unitig_749.g13708' => 'ugi', 'vmacro01063' => 'vma', 'VMungo0464G1086' => 'vmu', 'VMungo0464G1148' => 'vmu', 'VMungo0540G2214' => 'vmu', 'VMungo1309G2574' => 'vmu', 'VMungo1383G1422' => 'vmu', 'Zm00001eb157520' => 'zma', 'Zm00001eb159200' => 'zma', 'Zm00001eb347320' => 'zma', 'Zm00001eb358870' => 'zma', 'Zm00001eb418370' => 'zma' ) $gf_id = 'HOM05D001132' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001132' ) $data_identifier = 'HOM05D001132' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 10, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 6, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 2, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 17, 'gra' => (int) 11, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 5, 'nta' => (int) 5, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 6, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 1, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 7, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 39, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 1, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418370' $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